rs7902155

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001363545.2(PFKFB3):​c.1516-7386T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,204 control chromosomes in the GnomAD database, including 2,106 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2106 hom., cov: 31)

Consequence

PFKFB3
NM_001363545.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.705
Variant links:
Genes affected
PFKFB3 (HGNC:8874): (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3) The protein encoded by this gene belongs to a family of bifunctional proteins that are involved in both the synthesis and degradation of fructose-2,6-bisphosphate, a regulatory molecule that controls glycolysis in eukaryotes. The encoded protein has a 6-phosphofructo-2-kinase activity that catalyzes the synthesis of fructose-2,6-bisphosphate (F2,6BP), and a fructose-2,6-biphosphatase activity that catalyzes the degradation of F2,6BP. This protein is required for cell cycle progression and prevention of apoptosis. It functions as a regulator of cyclin-dependent kinase 1, linking glucose metabolism to cell proliferation and survival in tumor cells. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PFKFB3NM_001363545.2 linkuse as main transcriptc.1516-7386T>G intron_variant
PFKFB3XM_047425341.1 linkuse as main transcriptc.1455+20427T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PFKFB3ENST00000640683.1 linkuse as main transcriptc.1516-7386T>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.156
AC:
23755
AN:
152086
Hom.:
2106
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0818
Gnomad AMI
AF:
0.116
Gnomad AMR
AF:
0.118
Gnomad ASJ
AF:
0.293
Gnomad EAS
AF:
0.0873
Gnomad SAS
AF:
0.124
Gnomad FIN
AF:
0.227
Gnomad MID
AF:
0.174
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.161
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23759
AN:
152204
Hom.:
2106
Cov.:
31
AF XY:
0.156
AC XY:
11594
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0816
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.293
Gnomad4 EAS
AF:
0.0869
Gnomad4 SAS
AF:
0.124
Gnomad4 FIN
AF:
0.227
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.162
Alfa
AF:
0.184
Hom.:
1845
Bravo
AF:
0.146
Asia WGS
AF:
0.114
AC:
398
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.5
DANN
Benign
0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7902155; hg19: chr10-6288755; API